Only logical reason I've red about this 6 diff maximum is that having for example about 12 diffs would make really likely than some mistakes won't be seen until the map gets ranked. Apparently you can't just go and unrank one diff but have to unrank the whole set which is ridiculous but it works like that, so having 12 maps getting unranked because some mistake slipped out in some diff sucks.
And the limit is actually good enough if you don't allow any kind of guest diff. There are AWESOME mapsets like
http://osu.ppy.sh/s/29454 that everyone pretty much gave up in ranking because of this rule. Sometimes you make a map with those 5 standar difficulties like Easy, Normal, Hard, Insane, Lunatic. Someone goes and maybe maps two taiko diffs which is cool and then you get offered 2 guest diffs from nice mappers who happened to like the song, you end up with almost 10 diffs and your mapset can't get ranked because... it has more than 6 diffs and that's all? The limit is clearly not enough I think. Of course making the limit go to 12 or 20 or unlimited would make mapsets to be like: E N H I I I I I I I I I I I. But then again it's either that or the same song getting ranked 2 or 3 times for no real reason.
This rule is also related with the "no more than 3 insanes rules", since I think whenever this 6 limit is broken it's because there are lots of insanes, which is expected since you can be creative and map some fun Insane, but when mapping E or N you can't really do much.